---
title: "Bioconductor Package Vignette"
author: "Tsu-Pei Chiu, Federico Comoglio and Remo Rohs"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
    %\VignetteIndexEntry{DNAshapeR}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

## Introduction

DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput 
manner from genomic sequencing data. The package takes either nucleotide 
sequence or genomic intervals as input, and generates various graphical 
representations for further analysis. DNAshapeR further encodes DNA 
sequence and shape features for statistical learning applications by 
concatenating feature matrices with user-defined combinations of k-mer 
and DNA shape features that can be readily used as input for machine 
learning algorithms.

In this vignette, you will learn: 

* how to load/install DNAshapeR

* how to predict DNA shape features

* how to visualize DNA shape predictions

* how to encode sequence and shape features, and apply them


## Load DNAshapeR

```{r eval=TRUE}
library(DNAshapeR)
```

## Predict DNA shape features
The core of DNAshapeR, the DNAshape method (Zhou, et al., 2013), 
uses a sliding pentamer window where structural features unique 
to each of the 512 distinct pentamers define a vector of minor 
groove width (MGW), Roll, propeller twist (ProT), and helix twist 
(HelT) at each nucleotide position. MGW and ProT define base-pair 
parameters whereas Roll and HelT represent base pair-step parameters. 
The values for each DNA shape feature as function of its pentamer 
sequence were derived from all-atom Monte Carlo simulations where DNA 
structure is sampled in collective and internal degrees of freedom in 
combination with explicit sodium counter ions (Zhang, et al., 2014). 
The Monte Carlo simulations were analyzed with a modified Curves 
approach (Zhou, et al., 2013). Average values of each shape feature 
for each pentamer were derived from analyzing the ensemble of Monte 
Carlo predictions for 2,121 DNA fragments of 12−27 base pairs in length. 
DNAshapeR predicts the four DNA shape features MGW, HelT, ProT, and Roll, 
which were observed in various cocrystal structures as playing an important 
role in specific protein-DNA binding. 

In the latest version, we further added additional 9 DNA shape features 
beyond our previous set of 4 features, and expanded our available 
repertoire to a total of 13 features, including 6 inter-base pair or 
base pair-step parameters (HelT, Rise, Roll, Shift, Slide, and Tilt), 
6 intra-base pair or base pair-step parameters (Buckle, Opening, ProT, 
Shear, Stagger, and Stretch), and MGW.


## Predict biophysical feature
Our previous work explained protein-DNA binding specificity based on 
correlations between MGW and (electrostatic potential) EP observed in 
experimentally available structures (Joshi, et al., 2007). However, A/T 
and C/G base pairs carry different partial charge distributions in the 
minor groove (due primarily to the guanine amino group), which will affect 
minor-groove EP. We developed a high-throughput method, named DNAphi, to 
predict minor-groove EP based on data mining of results from solving the 
nonlinear Poisson-Boltzmann calculations (Honig & Nicholls, 1995) on 2,297 
DNA structures derived from Monte Carlo simulations. DNAshapeR includes EP 
as an additional feature.


## Predict DNA shape feature due to CpG methylation
To achieve a better mechanistic understanding of the effect of CpG 
methylation on local DNA structure, we developed a high-throughput 
method, named methyl-DNAshape, for predicting the impact of cytosine 
methylation on DNA shape features. In analogy to the DNAshape method 
(Zhou, et al., 2013), the method predicts DNA shape features (ProT, 
HelT, Roll, and MGW) in the context of CpG methylation based on 
methyl-DNAshape Pentamer Query Table (mPQT) derived from the results 
of all-atom Monte Carlo simulations on a total of 3,518 DNA fragments 
of lengths varying from 13 to 24 bp.  



DNAshapeR can predict DNA shape features from custom FASTA files or directly 
from genomic coordinates in the form of a GRanges object within Bioconductor 
(see <https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html> 
for more information). 

### From FASTA file

To predict DNA shape features from a FASTA file

```{r eval=TRUE}
library(DNAshapeR)
fn <- system.file("extdata", "CGRsample.fa", package = "DNAshapeR")
pred <- getShape(fn)
```

### From genomic intervals (e.g. TFs binding sites, CpG islands, replication origins, ...)

To predict DNA shape from genomic intervals stored as GRanges object, a 
reference genome is required. Several reference genomes are available 
within BioConductor as BSgenome objects 
(see <http://bioconductor.org/packages/release/bioc/html/BSgenome.html> 
for more information). For example, the sacCer3 release of the *S.Cerevisiae* 
genome can be retrieved. Given a reference genome, the **getFasta** function 
first extracts the DNA 
sequences based on the provided genomic coordinates, and then performs shape 
predictions within a user-defined window (of size equal to width, 100 bp in 
the example below) computed from the center of each genomic interval:

```{r eval=FALSE}
# Install Bioconductor packages
source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Scerevisiae.UCSC.sacCer3")

library(BSgenome.Scerevisiae.UCSC.sacCer3)

# Create a query GRanges object
gr <- GRanges(seqnames = c("chrI"),
            strand = c("+", "-", "+"),
            ranges = IRanges(start = c(100, 200, 300), width = 100))
getFasta(gr, Scerevisiae, width = 100, filename = "tmp.fa")
fn <- "tmp.fa"
pred <- getShape(fn)
```

### From public domain projects

The genomic intervals can also be obtained from public domain projects, 
including ENCODE, NCBI, Ensembl, etc. The AnnotationHub package 
(see <http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html> 
for more information) provides an interface to retrieve genomic intervals 
from these multiple online project resources.The genomic intervals of interest
can be selected progressively through the functions of **sebset** and **query** 
with keywords, and can be subjected as 
an input of GRanges object to **getFasta** function.

```{r eval=FALSE}
# Install Bioconductor packages
library(BSgenome.Hsapiens.UCSC.hg19)
library(AnnotationHub)

ah <- AnnotationHub()
ah <- subset(ah, species=="Homo sapiens")
ah <- query(ah, c("H3K4me3", "Gm12878", "Roadmap"))
getFasta(ah[[1]], Hsapiens, width = 150, filename = "tmp.fa")
fn <- "tmp.fa"
pred <- getShape(fn)
```


### From FASTA file with methylated DNA sequence

To predict DNA shape features in the context of CpG methylation, one 
can prepare a FASTA file of sequence with symbol ‘Mg’: ‘M’ referring 
to cytosine of methylated CpG on the leading strand and ‘g’ referring 
the cytosine of methylated CpG on lagging strand. For example,

\>seq1

GTGTCACMgCGTCTATACG

notifying the cytosine at position 8th on the leading strand and the 
one at position 9th on the lagging strand are methylated.

```{r eval=TRUE}
library(DNAshapeR)
fn_methy <- system.file("extdata", "MethylSample.fa", package = "DNAshapeR")
pred_methy <- getShape(fn_methy, methylate = TRUE)
pred_methy$MGW
```


### From FASTA and methylated position files

To predict DNA shape features in the context of CpG methylation, 
in addition to providing regular FASTA file (without symbolizing ‘Mg’) 
one can provide an additional input file identifying methylated positions. 
For example, 

\>seq1

4,16

notifying the cytosine at position 4th and 16th on leading strand, and 5th 
and 17th on lagging strand are methylated.


```{r eval=TRUE}
library(DNAshapeR)
fn_methy <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR")
fn_methy_pos <- system.file("extdata", "MethylSamplePos.fa", package = "DNAshapeR")
pred_methy <- getShape(fn_methy, methylate = TRUE, methylatedPosFile = fn_methy_pos)
pred_methy$MGW
```


## Visualize DNA shape prediction
DNAshapeR can be used to generate various graphical representations for 
further analyses. The prediction result can be visualized in the form of 
scatter plots (Comoglio, et al., 2015), heat maps (Yang, et al., 2014), 
or genome browser tracks (Chiu, et al., 2015).

### Ensemble representation: metashape plot
The prediction result can be visualized in the metaprofiles of DNA shape 
features.

```{r fig.width=7, fig.height=7, fig.align='center', eval=TRUE}
plotShape(pred$MGW)
#plotShape(pred$ProT)
#plotShape(pred$Roll)
#plotShape(pred$HelT)
```

### Ensemble representation: heat map
The prediction result can be visualized in the heatmap of DNA shape features.

```{r fig.width=7, fig.height=7, fig.align='center', eval=TRUE}
library(fields)
heatShape(pred$ProT, 20)
#heatShape(pred$MGW, 20)
#heatShape(pred$Roll[1:500, 1:1980], 20)
#heatShape(pred$HelT[1:500, 1:1980], 20)
```


### Individual representation: genome browser-like tracks
The prediction result can be visualized in the form of genome browser tracks.

*Note that the input data should only contain one sequence.

```{r fig.width=7, fig.height=7, fig.align='center', eval=TRUE}
fn2 <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR")
pred2 <- getShape(fn2)
trackShape(fn2, pred2) # Only for single sequence file
```

## Encode sequence and shape features
DNAshapeR can be used to generate feature vectors for a user-defined model. 
These models can consist of either sequence features (1-mer, 2-mer, 3-mer), 
shape features (MGW, Roll, ProT, HelT), or any combination of those two. 
For 1-mer features, sequence is encoded in form of four binary numbers 
(i.e., in terms of 1-mers, 1000 for adenine, 0100 for cytosine, 0010 for 
guanine, and 0001 for thymine) at each nucleotide position (Zhou, et al., 
2015). The encoding function of the DNAshapeR package enables the 
determination of higher order sequence features, for example, 2-mers and 
3-mers (16 and 64 binary features at each position, respectively). The 
user can also choose to include second order shape features in the 
generated feature vector. The second order shape features are product 
terms of values for the same category of shape features (MGW, Roll, ProT or 
HelT) at adjacent positions. The feature encoding function of DNAshapeR 
enables the generation of any subset of these features, either only a 
selected shape category or first order shape features, and any combination 
with shape or sequence features. The result of feature encoding for each 
sequence is a chimera feature vector.

### Encoding process
A feature type vector should be defined before encoding. The vector can be
any combination of characters of “k-mer”, “n-shape”, “n-MGW”, “n-ProT”, 
“n-Roll”, “n-HelT” (k, n are integers) where “1-shape” refers to first 
order and “2-shape” to second order shape features.

```{r eval=TRUE}
library(Biostrings)
fn3 <- system.file("extdata", "PBMsample_short.fa", package = "DNAshapeR")
pred3 <- getShape(fn3)
featureType <- c("1-mer", "1-shape")
featureVector <- encodeSeqShape(fn3, pred3, featureType)
head(featureVector)
```

### Showcase of statistical machine learning application
Feature encoding of multiple sequences thus results in a feature matrix, 
which can be used as input for variety of statistical machine learning 
methods. For example, an application is the quantitative modeling of 
PBM derived protein-DNA binding by linear regression as demonstrated 
below.

First, pre-computed binding affinity values are combined with experimental 
information in a data frame structure.

```{r eval=TRUE}
fn4 <- system.file("extdata", "PBMsample_short.s", package = "DNAshapeR")
experimentalData <- read.table(fn4)
df <- data.frame(affinity=experimentalData$V1, featureVector)
```

Then, a machine learning package (which can be any learning tools) is used 
to train a multiple linear regression (MLR) model based on 3-fold 
cross-validation. In this example, we used the caret package 
(see <http://caret.r-forge.r-project.org/> for more information).

```{r eval=TRUE}
library(caret)

trainControl <- trainControl(method = "cv", number = 3, 
                savePredictions = TRUE)
model <- train (affinity~ ., data = df, 
                trControl=trainControl, method="lm", preProcess=NULL)
model
```


## Session Info
```{r eval=TRUE}
sessionInfo()
```

## References


Chiu, T.P., et al. GBshape: a genome browser database for DNA shape 
annotations. Nucleic Acids Res 2015.

Comoglio, F., et al. High-resolution profiling of Drosophila replication 
start sites reveals a DNA shape and chromatin signature of metazoan origins. 
Cell reports 2015;11(5):821-834.

Yang, L., et al. TFBSshape: a motif database for DNA shape features of 
transcription factor binding sites. Nucleic Acids Res 2014;42
(Database issue):D148-155.

Zhou, T., et al. DNAshape: a method for the high-throughput prediction of
DNA structural features on a genomic scale. Nucleic Acids Res 2013;41
(Web Server issue):W56-62.

If you use DNAshapeR for your work, please cite the following publication:

Chiu, T-P., et al. DNAshapeR: an R/Bioconductor package for DNA shape 
prediction and feature encoding (2016).



